[gmx-users] Re: Born-Mayer-Huggins type pair potential
Hi! I would like to simulate halkali halides in GROMACS by using the Tosi-Fumi potential. The potential is of this kind (Born Mayer Huggins), with an exponential, a 6th, 8th powers and the coulomb term: U(r) = Ae^(-r/rho) - C/r^6 -D/r^8 + (q1 q2)/(4 pi eps r) Did somebody used anything of this kind? Is there a way to use this potential in GROMACS? Do you have any suggestions? Tabulate it. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Invitation to connect on LinkedIn
LinkedIn Ramachandran Gnanasekaran requested to add you as a connection on LinkedIn: -- Chinmay, I'd like to add you to my professional network on LinkedIn. - Ramachandran Accept invitation from Ramachandran Gnanasekaran http://www.linkedin.com/e/-85v1n9-hegpwiub-1v/Xl9gjr6GAOlB4vIjeR9gqTUPRTlBoITTu0/blk/I485341091_16/0UcDpKqiRzolZKqiRybmRSrCBvrmRLoORIrmkZt5YCpnlOt3RApnhMpmdzgmhxrSNBszYSclYNej0Nd3cRe3h9bS4PcBtAmyQNbPgSdjoQe34Qdj8LrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=falsetok=0rU2MOqpU9PlE1 View profile of Ramachandran Gnanasekaran http://www.linkedin.com/e/-85v1n9-hegpwiub-1v/rso/110455680/Tewa/name/15686615_I485341091_16/?hs=falsetok=2V8dXf5bs9PlE1 -- You are receiving Invitation emails. This email was intended for Chinmay Das. Learn why this is included: http://www.linkedin.com/e/-85v1n9-hegpwiub-1v/plh/http%3A%2F%2Fhelp%2Elinkedin%2Ecom%2Fapp%2Fanswers%2Fdetail%2Fa_id%2F4788/-GXI/?hs=falsetok=0K91Q5MZ09PlE1 (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .top file from .tpr and .xtc
Hi, if you were able to obtain a simulation it means you had a valid .top file! In any case, gromacs recognises disulfide basing on the distance beween the SG atoms. In addition, the two chains are supposed to be in the same molecule. So, my advice is, remove all the TER from pdb (but the last one), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] cuda gpu status on mdrun
Hi, I am new to gromacs and started playing a bit on my laptop (Lenovo Y510, Geforce 8400M GT) running ubuntu 12.10 with cuda 5.0. Everything is working well, gromacs does not complain about anything. But sometimes when using mdrun at start the gpu status is insane. What does that mean ? Thank you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] simulating only few residues from whole protein]
Original Message Subject: simulating only few residues from whole protein From:preetichoudh...@iisermohali.ac.in Date:Tue, March 19, 2013 10:45 am To: gmx-users@gromacs.org -- Original Message Subject: From:preetichoudh...@iisermohali.ac.in Date:Tue, March 19, 2013 10:44 am To: gmx-users@gromacs.org -- Hi, can anyone tell me how to carry out simulations in which we take the whole protein pdb structure but simulate only a certain part of it(only some residues). what will be the mdp files for such simulations ??? please help me if you know how to do it. -thankyou -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .top file from .tpr and .xtc
Thanks Francesco. But my problem is exactly opposite. I do have a .top file containing both chain linked by disulfide bridge. I ran the simulation. Now I have extracted .xtc file for each chain separately and I want the corresponding, separate .top file for each chain. when I separate the pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is absent in .xtc file. So the .top file generated this way has one atom more as compared to .xtc file. shahid On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri francesco.ot...@gmail.com wrote: Hi, if you were able to obtain a simulation it means you had a valid .top file! In any case, gromacs recognises disulfide basing on the distance beween the SG atoms. In addition, the two chains are supposed to be in the same molecule. So, my advice is, remove all the TER from pdb (but the last one), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] .top file from .tpr and .xtc
Could you simply edit the file and removing the atom from [atoms] section ? grompp wil complain regarding the line containing interactions. But also these few lines can be removed. Otherwise, vmd has the TopoTools that write the .top topology of the loaded pdb. Unfortunately, this topologyes are not useful for carrying out MD because they lack parameters. In any case are good for analysis! Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Thanks Francesco. But my problem is exactly opposite. I do have a .top file containing both chain linked by disulfide bridge. I ran the simulation. Now I have extracted .xtc file for each chain separately and I want the corresponding, separate .top file for each chain. when I separate the pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is absent in .xtc file. So the .top file generated this way has one atom more as compared to .xtc file. shahid On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri francesco.ot...@gmail.com wrote: Hi, if you were able to obtain a simulation it means you had a valid .top file! In any case, gromacs recognises disulfide basing on the distance beween the SG atoms. In addition, the two chains are supposed to be in the same molecule. So, my advice is, remove all the TER from pdb (but the last one), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read
Re: [gmx-users] .top file from .tpr and .xtc
I did it. Simply I changed the name of Cys which forms interchain dsiulfide bond to CYS2 in the separated pdb file and I used G43a1 forcefeild to run pdb2gmx. This gives a topology with same number of atom which is present in .xtc file. CYS2 is present .rtp file of G43a1 forcefeild probably to form interchain disulfide bond reading from specbond.dat. Am I right in generating such half disulfide bond topology. shahid On Tue, Mar 19, 2013 at 2:10 PM, francesco oteri francesco.ot...@gmail.com wrote: Could you simply edit the file and removing the atom from [atoms] section ? grompp wil complain regarding the line containing interactions. But also these few lines can be removed. Otherwise, vmd has the TopoTools that write the .top topology of the loaded pdb. Unfortunately, this topologyes are not useful for carrying out MD because they lack parameters. In any case are good for analysis! Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Thanks Francesco. But my problem is exactly opposite. I do have a .top file containing both chain linked by disulfide bridge. I ran the simulation. Now I have extracted .xtc file for each chain separately and I want the corresponding, separate .top file for each chain. when I separate the pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is absent in .xtc file. So the .top file generated this way has one atom more as compared to .xtc file. shahid On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri francesco.ot...@gmail.com wrote: Hi, if you were able to obtain a simulation it means you had a valid .top file! In any case, gromacs recognises disulfide basing on the distance beween the SG atoms. In addition, the two chains are supposed to be in the same molecule. So, my advice is, remove all the TER from pdb (but the last one), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] .top file from .tpr and .xtc
If it works then you are right :) 2013/3/19 shahid nayeem msnay...@gmail.com I did it. Simply I changed the name of Cys which forms interchain dsiulfide bond to CYS2 in the separated pdb file and I used G43a1 forcefeild to run pdb2gmx. This gives a topology with same number of atom which is present in .xtc file. CYS2 is present .rtp file of G43a1 forcefeild probably to form interchain disulfide bond reading from specbond.dat. Am I right in generating such half disulfide bond topology. shahid On Tue, Mar 19, 2013 at 2:10 PM, francesco oteri francesco.ot...@gmail.com wrote: Could you simply edit the file and removing the atom from [atoms] section ? grompp wil complain regarding the line containing interactions. But also these few lines can be removed. Otherwise, vmd has the TopoTools that write the .top topology of the loaded pdb. Unfortunately, this topologyes are not useful for carrying out MD because they lack parameters. In any case are good for analysis! Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Thanks Francesco. But my problem is exactly opposite. I do have a .top file containing both chain linked by disulfide bridge. I ran the simulation. Now I have extracted .xtc file for each chain separately and I want the corresponding, separate .top file for each chain. when I separate the pdb and run the pdb2gmx I get one hydrogen on SG atom of Cys which is absent in .xtc file. So the .top file generated this way has one atom more as compared to .xtc file. shahid On Tue, Mar 19, 2013 at 1:07 PM, francesco oteri francesco.ot...@gmail.com wrote: Hi, if you were able to obtain a simulation it means you had a valid .top file! In any case, gromacs recognises disulfide basing on the distance beween the SG atoms. In addition, the two chains are supposed to be in the same molecule. So, my advice is, remove all the TER from pdb (but the last one), leave the chain id and use pdb2gmx with the option -chainsep ter. The result is supposed to be a topology where your chain are grouped in a single molecule,making possible to create the bridge, and at the same time you keep the chain name for future analysis. Francesco 2013/3/19 shahid nayeem msnay...@gmail.com Hi To be more clear I have .xtc file for a disulfide linked complex of two chains. From this trajectory I can extract .xtc file for individual chains. But when I generate .top file from individual chain pdb I get one atom extra in .top file i.e. protonated SG of Cys which I dont need in order to make my .xtc and .top file compatible. Shahid On Tue, Mar 19, 2013 at 2:07 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 12:35 PM, shahid nayeem wrote: Hi Is it possible to write .top file from .xtc and .tpr using index.ndx so that .top is available for tailormade components of simulated protein. All topology information is in the .tpr, but not in .top format. You may be able to post-process the output of gmxdump to produce some hacked version, but that's just a bit of a hand-waving guess. I don't really understand what your objective is. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org
[gmx-users] Freezing some residues in equillibrium state?
Anyone tell me how do I freeze the particular residues in NPT-NVT equillibrium steps ? I want them in same conformation as pdb for further production run ? Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Desired density - genbox
Thanks. So in this case no matter what density I will start with e.g. 480 kg/m3 presuming the force filed is correct I should get at given conditions the density of interest? Steven On Mon, Mar 18, 2013 at 10:34 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 6:14 PM, Steven Neumann wrote: On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 2:56 PM, Steven Neumann wrote: Dear Gmx Users, I am trying to obtain given density for my system for a given molecule - its a cubic box of 5 nm in dimension. I calculated that I need 850 molecules to get the density of 500 g/mol In my box there is already 1 molecule so I try: genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb Added 819 molecules (out of 849 requested) Output configuration contains 9020 atoms in 820 residues Volume : 125 (nm^3) Density: 480.336 (g/l) Number of SOL molecules: 0 How can I add 30 more molecules using gromacs? I want to avoid adding it manually. Use a larger box and equilibrate. Thanks. Larger box will need more molecules which is quite obvious so the same problem occurs. I need a cubic box first with given fixed density and then equilibrate it. Further step is to extend the box in one dimension to get properties I want. Shall manually add them then? I think you missed the point of what I was saying. You can use a larger box, with 850 molecules inserted, and equilbrate under NPT (using isotropic pressure coupling to guarantee the box stays cubic). Provided the force field model produces the density you want, that's all you need to do. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Desired density - genbox
On 3/19/13 5:52 AM, Steven Neumann wrote: Thanks. So in this case no matter what density I will start with e.g. 480 kg/m3 presuming the force filed is correct I should get at given conditions the density of interest? If the force field has been parametrized to reproduce the density, then yes. -Justin On Mon, Mar 18, 2013 at 10:34 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 6:14 PM, Steven Neumann wrote: On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul jalem...@vt.edu wrote: On 3/18/13 2:56 PM, Steven Neumann wrote: Dear Gmx Users, I am trying to obtain given density for my system for a given molecule - its a cubic box of 5 nm in dimension. I calculated that I need 850 molecules to get the density of 500 g/mol In my box there is already 1 molecule so I try: genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb Added 819 molecules (out of 849 requested) Output configuration contains 9020 atoms in 820 residues Volume : 125 (nm^3) Density: 480.336 (g/l) Number of SOL molecules: 0 How can I add 30 more molecules using gromacs? I want to avoid adding it manually. Use a larger box and equilibrate. Thanks. Larger box will need more molecules which is quite obvious so the same problem occurs. I need a cubic box first with given fixed density and then equilibrate it. Further step is to extend the box in one dimension to get properties I want. Shall manually add them then? I think you missed the point of what I was saying. You can use a larger box, with 850 molecules inserted, and equilbrate under NPT (using isotropic pressure coupling to guarantee the box stays cubic). Provided the force field model produces the density you want, that's all you need to do. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Freezing some residues in equillibrium state?
On 3/19/13 5:44 AM, 라지브간디 wrote: Anyone tell me how do I freeze the particular residues in NPT-NVT equillibrium steps ? I want them in same conformation as pdb for further production run ? Thanks in advance Use freezegrps or strong position restraints. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] simulating only few residues from whole protein]
On 3/19/13 4:13 AM, preetichoudh...@iisermohali.ac.in wrote: Original Message Subject: simulating only few residues from whole protein From:preetichoudh...@iisermohali.ac.in Date:Tue, March 19, 2013 10:45 am To: gmx-users@gromacs.org -- Original Message Subject: From:preetichoudh...@iisermohali.ac.in Date:Tue, March 19, 2013 10:44 am To: gmx-users@gromacs.org -- Hi, can anyone tell me how to carry out simulations in which we take the whole protein pdb structure but simulate only a certain part of it(only some residues). what will be the mdp files for such simulations ??? please help me if you know how to do it. Do you want to extract certain residues from the structure and simulate those, or just try to fix the positions of some residues while allowing others to move? In the latter case, use freezegrps or position restraints. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] About Detrium order Parameter
Dear Justin Thank you for your Previous Reply I am following you Protein Lipid Tutorial . In Analysis Part I Have Done Deuterium Order Parameters Analysis using index files . Kindly brief About Deuterium order parameter Analysis From the Graph How to interpret and Conclude Result ? Thanks in Advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About Detrium order Parameter
On 3/19/13 6:59 AM, vidhya sankar wrote: Dear Justin Thank you for your Previous Reply I am following you Protein Lipid Tutorial . In Analysis Part I Have Done Deuterium Order Parameters Analysis using index files . Kindly brief About Deuterium order parameter Analysis From the Graph How to interpret and Conclude Result ? Study the literature and draw your own conclusions. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] trjconv centre protein
Hi, I know this question has been asked for a few times already but I don't seem to get it. :( I did: 1) editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt dodecahedron 2) genbox -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top 3) grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr and then I view the solv.gro file in VMD and found out that the protein is hanging out from the box as in the attached image: http://postimage.org/image/6df12u991/ I tried to put it in the centre with the command: 4) trjconv -s ions.tpr -f solv.gro -o solvcentre.gro -pbc mol -ur compact But it shows that the protein (solvcentre.gro) is still the same (hanging out from the box). Did I overlook something? Can I proceed with EM? Please advice. :( Thanking you in advance! Best regards -- View this message in context: http://gromacs.5086.n6.nabble.com/trjconv-centre-protein-tp5006454.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] trjconv centre protein
On 3/19/13 7:44 AM, Ewaru wrote: Hi, I know this question has been asked for a few times already but I don't seem to get it. :( I did: 1) editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt dodecahedron 2) genbox -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top 3) grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr and then I view the solv.gro file in VMD and found out that the protein is hanging out from the box as in the attached image: http://postimage.org/image/6df12u991/ I tried to put it in the centre with the command: 4) trjconv -s ions.tpr -f solv.gro -o solvcentre.gro -pbc mol -ur compact But it shows that the protein (solvcentre.gro) is still the same (hanging out from the box). Did I overlook something? Can I proceed with EM? There is no outside of a periodic box. The system is infinite, so you can of course proceed with EM. If you want to center the protein, I would suggest using the -center option of trjconv to your command #4 above; that's what it does. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: trjconv centre protein
HI Justin, Thanks for the prompt reply! :) Correct me if I'm wrong, but I thought the protein has to be in the center (inside the box) before the simulation, is it? Thank you. Best regards. -- View this message in context: http://gromacs.5086.n6.nabble.com/trjconv-centre-protein-tp5006454p5006456.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Freezing some residues in equillibrium state?
On Mar 19, 2013, at 11:45 AM, Justin Lemkul wrote: On 3/19/13 5:44 AM, 라지브간디 wrote: Anyone tell me how do I freeze the particular residues in NPT-NVT equillibrium steps ? I want them in same conformation as pdb for further production run ? Thanks in advance Use freezegrps or strong position restraints. But note that if you release frozen groups after equilibration your system may need further time to equilibrate. Erik -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: trjconv centre protein
On 3/19/13 8:00 AM, Ewaru wrote: HI Justin, Thanks for the prompt reply! :) Correct me if I'm wrong, but I thought the protein has to be in the center (inside the box) before the simulation, is it? Absolutely not. In a periodic system, there is no such thing as a center. Centering within the central unit cell is merely a visualization convenience. The MD algorithm could care less. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: trjconv centre protein
Crystal clear! Thank you Justin! :) Take care. Regards. -- View this message in context: http://gromacs.5086.n6.nabble.com/trjconv-centre-protein-tp5006454p5006459.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Energy minimization failure
Greetings, I am relatively new to MD, and I am attempting to simulate a metal-organic framework but I don't seem to be even able to get past the energy minimization phase. I could appreciate any insight into what I might be doing wrong. Here is a brief summary of what I have done: - constructed a PDB file from the crystal structure coordinates of a model compound, capping the organic linker with phenyl and capping the metal atoms with water and hydroxide ions to yield a full coordination sphere and to yield a net charge of zero - constructed a custom force field using published parameters - run pdb2gmx to construct the .gro and .top files - run editconf to construct a box around the MOF, 5 nm in each dimension - run genbox to fill the box with water - run grompp to prepare the box for addition of ions - run genion to replace 20 solvent molecules with 10 Na+ and 10 Cl- ions - manually edit the topology file (per the suggestion here on the listserv of a few days ago) to include, in the [ pairs ] directive, all pair interactions for purposes of electrostatic computation, but with parameters of 0 0 for the van der Waals parameters, so as to have the van der Waals interactions remain the usual case of neglected for 1-2 and 1-3 interactions - create an index file containing a group that has the 60 atoms constituting the terminal water and hydroxide ion atoms, so as to keep their coordinates frozen during the minimization - run grompp again to prepare the box for energy minimization (below is the minim.mdp file used for this) - run mdrun to perform the energy minimization The energy minimization does not yield the maximum force falling below the desired 1000, but stays as high as 10^6. Visualization of the output .gro file yields that many atoms within the core of the MOF have moved into strange positions, i.e., the formation of seeming O-O bonds between adjacent carboxylates when instead both O atoms should be coordinated to the metal atom. The calculations yielded a great deal of data, and so as not to clog everybody's inboxes, I only included the one that seemed most relevant (minim.mdp). If there is something else required, I'll happily share it. I am not sure what's going on and I could appreciate any insight into what might be causing this and how to fix it. Thanks in advance , Jeff Woodford Assistant Professor of Chemistry Missouri Western State University minim.mdp: ; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.5 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.5 ; Short-range electrostatic cut-off rvdw = 1.5 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions (yes/no) freezegrps = Terminal_atoms freezedim = Y Y Y -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Energy minimization failure
On Tue, Mar 19, 2013 at 9:16 AM, Jeff Woodford jwoodf...@missouriwestern.edu wrote: Greetings, I am relatively new to MD, and I am attempting to simulate a metal-organic framework but I don't seem to be even able to get past the energy minimization phase. I could appreciate any insight into what I might be doing wrong. Here is a brief summary of what I have done: - constructed a PDB file from the crystal structure coordinates of a model compound, capping the organic linker with phenyl and capping the metal atoms with water and hydroxide ions to yield a full coordination sphere and to yield a net charge of zero - constructed a custom force field using published parameters - run pdb2gmx to construct the .gro and .top files - run editconf to construct a box around the MOF, 5 nm in each dimension - run genbox to fill the box with water - run grompp to prepare the box for addition of ions - run genion to replace 20 solvent molecules with 10 Na+ and 10 Cl- ions - manually edit the topology file (per the suggestion here on the listserv of a few days ago) to include, in the [ pairs ] directive, all pair interactions for purposes of electrostatic computation, but with parameters of 0 0 for the van der Waals parameters, so as to have the van der Waals interactions remain the usual case of neglected for 1-2 and 1-3 interactions - create an index file containing a group that has the 60 atoms constituting the terminal water and hydroxide ion atoms, so as to keep their coordinates frozen during the minimization - run grompp again to prepare the box for energy minimization (below is the minim.mdp file used for this) - run mdrun to perform the energy minimization The energy minimization does not yield the maximum force falling below the desired 1000, but stays as high as 10^6. Visualization of the output .gro file yields that many atoms within the core of the MOF have moved into strange positions, i.e., the formation of seeming O-O bonds between adjacent carboxylates when instead both O atoms should be coordinated to the metal atom. The calculations yielded a great deal of data, and so as not to clog everybody's inboxes, I only included the one that seemed most relevant (minim.mdp). If there is something else required, I'll happily share it. I am not sure what's going on and I could appreciate any insight into what might be causing this and how to fix it. I would suggest a few things: 1. Simplify as much as possible, using small units of structure to diagnose. 2. Look at various energy terms in the .edr file. One will likely stick out like a sore thumb in terms of being huge and positive, hence the large forces. My suspicion would be short-range Coulombic forces. Including nonbonded terms in 1-2 and 1-3 interactions is very weird, since they may oppose the normal bonded forces. The bonds you see forming are not actually there. Your visualization program is just guessing what's going on. It's certainly indicative of bad geometry, but no bonds are breaking or forming, unless you're doing QM and not telling us ;) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error during grompp run
Dear Users I am using groamcs 4.4.4 and when I run grompp during equilibration process, it closes with error Fatal error:Topology include file posre_Protein.itp not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors; However, I found Topology include file posre_Protein.itp in current directory. I am able to successfully run previous grompp during minimization, but I am facing this problem during equilibration only. Please help me to get rid of this issue. I welcome all suggestions. Thanks in advance Kshatresh Dutta Dubey -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] PMF and jacobian correction
Dear Gromacs user, I was having a question on when need to use jacobian coorection of -2KTln(r) ( gromacs manual chapter 6) term when calculating PMF. I understand for a 3-dimensional radial coordinate like distance between two groups, this term need to taken care of. But, if the PMF is computed along Radius of gyration which is an internal coordinate, I was wondering whether this jacobian correction still needs to be subtracted. Any help in sorting out this confusion will be appreciated. Sanku -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Top file modification
Dear users, I modified my top file, because I didn't want some bonds. So I deleted them and changed charges on some atoms. I want to go on with such a top file, however I am not sure that these changes are implemented properly or not. Would you please let me know if what I did is right or not? And how would I be sure about the proper modifications? Thanks in advance for all your beneficial suggestions. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error during grompp run
On Tue, Mar 19, 2013 at 10:46 AM, Kshatresh Dutta Dubey kshatr...@ymail.com wrote: Dear Users I am using groamcs 4.4.4 and when I run grompp during equilibration process, it closes with error Fatal error:Topology include file posre_Protein.itp not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors; However, I found Topology include file posre_Protein.itp in current directory. I am able to successfully run previous grompp during minimization, but I am facing this problem during equilibration only. Please help me to get rid of this issue. I welcome all suggestions. If grompp says it's not there, it's not there. Check carefully for typos in file names or #include statements as well as read permissions on the file itself. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Top file modification
On Tue, Mar 19, 2013 at 1:07 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Dear users, I modified my top file, because I didn't want some bonds. So I deleted them and changed charges on some atoms. I want to go on with such a top file, however I am not sure that these changes are implemented properly or not. Would you please let me know if what I did is right or not? And how would I be sure about the proper modifications? Making ad hoc changes to topologies or force fields is generally a bad idea unless you have thoroughly validated what you are doing with a correct parameterization procedure. What you've described above (especially given the lack of specificity) sounds very dangerous. If you want advice, be specific as to exactly what you are doing. It is your job to convince a skeptical audience (e.g., reviewers) that what you're doing makes sense and thus you must have strong justification for it. Somebody on the Internet told me it was OK is generally not an acceptable defense ;) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Top file modification
:) In fact, I have a NMR pdb file of a cyclic peptide. To get a proper gro and topology files, I ran pdb2gmx without -ter flag. Then tried to modify the top file. Is there any better ideas? Thanks for your reply. Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, March 19, 2013 8:51 PM Subject: Re: [gmx-users] Top file modification On Tue, Mar 19, 2013 at 1:07 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: Dear users, I modified my top file, because I didn't want some bonds. So I deleted them and changed charges on some atoms. I want to go on with such a top file, however I am not sure that these changes are implemented properly or not. Would you please let me know if what I did is right or not? And how would I be sure about the proper modifications? Making ad hoc changes to topologies or force fields is generally a bad idea unless you have thoroughly validated what you are doing with a correct parameterization procedure. What you've described above (especially given the lack of specificity) sounds very dangerous. If you want advice, be specific as to exactly what you are doing. It is your job to convince a skeptical audience (e.g., reviewers) that what you're doing makes sense and thus you must have strong justification for it. Somebody on the Internet told me it was OK is generally not an acceptable defense ;) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Top file modification
Would you please let me know if it is acceptable to add dihedrals and angles and bonds? and not to add any pairs to the top? just deleting the pairs which are added by pdb2gmx incorrectly to the terminus? And I don't know that if I don't add all bonds or dihedrals what would happen? How would I be sure that I have added all modifications completely? Sincerely, Shima From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com Sent: Tuesday, March 19, 2013 9:00 PM Subject: Re: [gmx-users] Top file modification On Tue, Mar 19, 2013 at 1:28 PM, Shima Arasteh shima_arasteh2...@yahoo.com wrote: :) In fact, I have a NMR pdb file of a cyclic peptide. To get a proper gro and topology files, I ran pdb2gmx without -ter flag. Then tried to modify the top file. Is there any better ideas? Manual modification in that case is probably reasonably safe, as long as you are careful to use parameters that are appropriate for all bonded and nonbonded interactions that change as a result of the modification. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Top file modification
On Tue, Mar 19, 2013 at 1:36 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Would you please let me know if it is acceptable to add dihedrals and angles and bonds? and not to add any pairs to the top? just deleting the pairs which are added by pdb2gmx incorrectly to the terminus? And I don't know that if I don't add all bonds or dihedrals what would happen? How would I be sure that I have added all modifications completely? All you're doing is creating a peptide bond like any other. Its description should be identical to any other peptide bond in the protein. An incorrect or incomplete description of the newly created peptide bond would mean an unreliable physical model that would either crash or produce spurious results. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Born-Mayer-Huggins type pair potential
Thank you! This is a very good suggestion. On Mon, Mar 18, 2013 at 11:49 PM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: Hi! I would like to simulate halkali halides in GROMACS by using the Tosi-Fumi potential. The potential is of this kind (Born Mayer Huggins), with an exponential, a 6th, 8th powers and the coulomb term: U(r) = Ae^(-r/rho) - C/r^6 -D/r^8 + (q1 q2)/(4 pi eps r) Did somebody used anything of this kind? Is there a way to use this potential in GROMACS? Do you have any suggestions? Tabulate it. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Function of dihedrals in top file
Dears, There is term of function for each 4 atoms in dihedral section in top file. How this function is defined? To add extra dihedrals manually, I need to add function too. Thanks. Sincerely, Shima -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Function of dihedrals in top file
As I found up to now, func 2 is related to improper dihedrals. How can I find improper dihedrals? Can I not add them? Sincerely, Shima - Original Message - From: Shima Arasteh shima_arasteh2...@yahoo.com To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, March 19, 2013 9:46 PM Subject: [gmx-users] Function of dihedrals in top file Dears, There is term of function for each 4 atoms in dihedral section in top file. How this function is defined? To add extra dihedrals manually, I need to add function too. Thanks. Sincerely, Shima -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Function of dihedrals in top file
On Tue, Mar 19, 2013 at 2:16 PM, Shima Arasteh shima_arasteh2...@yahoo.comwrote: Dears, There is term of function for each 4 atoms in dihedral section in top file. How this function is defined? To add extra dihedrals manually, I need to add function too. All of this information is in the manual, Chapters 4 (definition of functional forms) and 5 (implementation in the topology). Force field-specific concerns should be addressed in the literature. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] memory excess error of Tip4p/Ice model
Dear gromacs users I have performed MD simulation using Tip4p/ice model, which is copied from [http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_topology_file_for_the_TIP4P/Ice_model] The MD actually works and the output structure looks fine. However, after 11ns run, the run was suddenly stopped and I got the following error message. In case of Tip4p, in which .top file contains #include ffoplsaa.itp #include tip4p.itp the MD run works well and never stop, although I used the same .mdp and .gro file. The difference of two MD runs is just .top file, so I suspect .top file for tip4p/ice has something wrong. Could you please give me advise to fix it ? Regards Error tput: No value for $TERM and no -T specified = PBS: job killed: mem 33310024kb exceeded limit 32505856kb === .top file [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 no 1.0 1.0 [atomtypes] ;name mass charge ptypesigmaepsilon IW 0 0.000 D 0.0 0.0 OWT4 15.99940 0.000 A 0.31668 0.88211 HW 1.00800 0.000 A 0.0E+00 0.0E+00 [moleculetype] ; name nrexcl SOL 1 [atoms] ; nr type resnr residu atom cgnr charge 1 OWT4 1 water OW 1 0 15.994 2 HW 1 water HW1 1 0.58971.008 3 HW 1 water HW2 1 0.58971.008 4 IW 1 water MW 1-1.17940.0 [constraints] ;i j funct doh dhh 1 2 1 0.09572 1 3 1 0.09572 2 3 1 0.15139 [exclusions] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 [dummies3] ; Dummy fromfunct a b 4 1 2 3 1 0.13458 0.13458 [system] water TIP4P/Ice [molecules] SOL 433 = Kenji -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] memory excess error of Tip4p/Ice model
On 3/19/13 9:58 PM, Kenji Mochizuki wrote: Dear gromacs users I have performed MD simulation using Tip4p/ice model, which is copied from [http://www.sklogwiki.org/SklogWiki/index.php/GROMACS_topology_file_for_the_TIP4P/Ice_model] The MD actually works and the output structure looks fine. However, after 11ns run, the run was suddenly stopped and I got the following error message. In case of Tip4p, in which .top file contains #include ffoplsaa.itp #include tip4p.itp the MD run works well and never stop, although I used the same .mdp and .gro file. The difference of two MD runs is just .top file, so I suspect .top file for tip4p/ice has something wrong. Could you please give me advise to fix it ? Regards Error tput: No value for $TERM and no -T specified = PBS: job killed: mem 33310024kb exceeded limit 32505856kb === These messages are coming from your cluster's management system. You should consult your sysadmins; this is not a Gromacs problem. -Justin .top file [ defaults ] ; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ 1 2 no 1.0 1.0 [atomtypes] ;name mass charge ptypesigmaepsilon IW 0 0.000 D 0.0 0.0 OWT4 15.99940 0.000 A 0.31668 0.88211 HW 1.00800 0.000 A 0.0E+00 0.0E+00 [moleculetype] ; name nrexcl SOL 1 [atoms] ; nr type resnr residu atom cgnr charge 1 OWT4 1 water OW 1 0 15.994 2 HW 1 water HW1 1 0.58971.008 3 HW 1 water HW2 1 0.58971.008 4 IW 1 water MW 1-1.17940.0 [constraints] ;i j funct doh dhh 1 2 1 0.09572 1 3 1 0.09572 2 3 1 0.15139 [exclusions] 1 2 3 4 2 1 3 4 3 1 2 4 4 1 2 3 [dummies3] ; Dummy fromfunct a b 4 1 2 3 1 0.13458 0.13458 [system] water TIP4P/Ice [molecules] SOL 433 = Kenji -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: polymer duplicate atoms
I follow your advice to edit the bond conditions of residues Fbg and Fen in my rtp file. Subsequently, I should modify the hdb file to add hydrogens for Fbg and Fen. However, I get the fatal error message Atom +C1 not found in residue Fbg 113, rtp entry Fbg while adding hydrogens. I can successfully generate the structure (conf.gro) when I am using pdb2gmx command(pdb2gmx -ff oplsaa -f 2.pdb -q -missing) with the -missing option and ignoring the hdb file. ; rtp file [ Fbg ] [ bonds ] C5+C1 C5H51 C5H52 C5H53 [ Fen ] [ bonds ] C6-C4 C6H11 C6H12 C6H13 ; hdb file Fbg 1 3 4 H C5 +C1 +C2 Fen 1 3 4 H C6 -C4 -C3 f2311-differ_residue_num.pdb http://gromacs.5086.n6.nabble.com/file/n5006479/f2311-differ_residue_num.pdb -- View this message in context: http://gromacs.5086.n6.nabble.com/polymer-duplicate-atoms-tp5006328p5006479.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] RE: RE: covalent binding- Improper Dih (Emanuel Birru)
Dear Eb, Thanks for the reply and input! I have posted part of the bonded itp file as below. Could you please be kind to specify how to revise the multiplicity? Many thanks! BTW, the force field we used is Amber. Thanks again! Cheers Jeremy -- [ dihedraltypes ] ;i j k l func CT CT OS CT9 0.0 1.60247 3 ; CT CT OS CT9 180.0 0.41840 2 ; C N CT C 9 0.0 1.12968 2 ; new for 99sb C N CT C 9 0.0 1.75728 3 ; new for 99sb N CT C N 9 180.0 1.88280 1 ; new for 99sb N CT C N 9 180.0 6.61072 2 ; new for 99sb N CT C N 9 180.0 2.30120 3 ; new for 99sb CT CT N C 9 0.0 8.36800 1 ; new for 99sb CT CT N C 9 0.0 8.36800 2 ; new for 99sb CT CT N C 9 0.0 1.67360 3 ; new for 99sb CT CT C N 9 0.0 0.83680 1 ; new for 99sb CT CT C N 9 0.0 0.83680 2 ; new for 99sb CT CT C N 9 0.0 1.67360 3 ; new for 99sb H N C O 9 180.0 10.46000 2 ; JCC,7,(1986),230 H N C O 9 0.0 8.36800 1 ; J.C.cistrans-NMA DE CT S S CT9 0.0 14.64400 2 ; JCC,7,(1986),230 CT S S CT9 0.0 2.51040 3 ; JCC,7,(1986),230 OS CT CT OS9 0.0 0.60250 3 ; parm98, TC,PC,PAK OS CT CT OS9 0.0 4.91620 2 ; Piotr et al. OS CT CT OH9 0.0 0.60250 3 ; parm98, TC,PC,PAK OS CT CT OH9 0.0 4.91620 2 ; parm98, TC,PC,PAK OH CT CT OH9 0.0 0.60250 3 ; parm98, TC,PC,PAK OH CT CT OH9 0.0 4.91620 2 ; parm98, TC,PC,PAK OH P OS CT9 0.0 1.04600 3 ; JCC,7,(1986),230 OH P OS CT9 0.0 5.02080 2 ; gggt ene.631g*/mp2 OS P OS CT9 0.0 1.04600 3 ; JCC,7,(1986),230 OS P OS CT9 0.0 5.02080 2 ; gggt ene.631g*/mp2 OS CT N* CK9 0.0 10.46000 1 ; parm98, TC,PC,PAK OS CT N* CM9 0.0 10.46000 1 ; parm98, TC,PC,PAK H1 CT C O 9 0.0 3.34720 1 ; Junmei et al, 1999 H1 CT C O 9 180.0 0.33472 3 ; Junmei et al, 1999 HC CT C O 9 0.0 3.34720 1 ; Junmei et al, 1999 HC CT C O 9 180.0 0.33472 3 ; Junmei et al, 1999 HC CT CT HC9 0.0 0.62760 3 ; Junmei et al, 1999 HC CT CT CT9 0.0 0.66944 3 ; Junmei et al, 1999 HC CT CM CM9 180.0 1.58992 3 ; Junmei et al, 1999 HC CT CM CM9 0.0 4.81160 1 ; Junmei et al, 1999 HO OH CT CT9 0.0 0.66944 3 ; Junmei et al, 1999 HO OH CT CT9 0.0 1.04600 1 ; Junmei et al, 1999 HO OH C O 9 180.0 9.62320 2 ; Junmei et al, 1999 HO OH C O 9 0.0 7.94960 1 ; Junmei et al, 1999 CM CM C O 9 180.0 9.10020 2 ; Junmei et al, 1999 CM CM C O 9 0.0 1.25520 3 ; Junmei et al, 1999 CT CM CM CT9 180.0 27.82360 2 ; Junmei et al, 1999 CT CM CM CT9 180.0 7.94960 1 ; Junmei et al, 1999 CT CT CT CT9 0.0 0.75312 3 ; Junmei et al, 1999 CT CT CT CT9 180.0 1.04600 2 ; Junmei et al, 1999 CT CT CT CT9 180.0 0.83680 1 ; Junmei et al, 1999 CT CT OS C 9 0.0 1.60247 3 ; Junmei et al, 1999 CT CT OS C 9 180.0 3.34720 1 ; Junmei et al, 1999 CT OS CT OS9 0.0 0.41840 3 ; Junmei et al, 1999 CT OS CT OS9 180.0 3.55640 2 ; Junmei et al, 1999 CT OS CT OS9 180.0 5.64840 1 ; Junmei et al, 1999 O C OS CT9 180.0 11.29680 2 ; Junmei et al, 1999 O C OS CT9 180.0 5.85760 1 ; Junmei et al, 1999 F CT CT F 9 180.0 5.02080 1 ; Junmei et al, 1999 Cl CT CT Cl9 180.0 1.88280 1 ; Junmei et al, 1999 Br CT CT Br9 0.0 0.0 0 ; Junmei et al, 1999 H1 CT CT OS9 0.0 1.04600 1 ; Junmei et al, 1999 H1 CT CT OH9 0.0 1.04600 1 ; Junmei et al, 1999 H1 CT CT F 9 0.0 0.79496 1 ; Junmei et al, 1999 H1 CT CT Cl9 0.0 1.04600 1 ; Junmei et al, 1999 H1 CT CT Br9 0.0 2.30120 1 ; Junmei et al, 1999 HC CT CT OS9 0.0 1.04600 1 ; Junmei et al, 1999 HC CT CT OH9 0.0 1.04600 1 ; Junmei et al, 1999 HC CT CT F 9 0.0 0.79496 1 ; Junmei et al, 1999 HC CT CT Cl9 0.0 1.04600 1 ;
RE: [gmx-users] Re: polymer duplicate atoms
FYI, I only showed you the bond part of the residue in the previous email (since that was the section I was commenting on and showed how it should be there) there should be some atom details prior to that, as required by the rtp format. You need to use your own judgment and the manual to ensure it is the correct format for the entry etc. Plus, you have the atom naming all messed up now. It is not surprising you are getting an error saying that it can't find atom C1, since the Fbg residue does not have any, you have named it C5. How have to use the same naming convention as you do with the polymer monomer unit, otherwise you wont be able to automatically cap it. Another option is to have a Fbg and Fen that includes a capped monomer unit, rather than just the methyl group. That may be a better way to go about it. Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of cqgzc Sent: Wednesday, 20 March 2013 1:24 PM To: gmx-users@gromacs.org Subject: [gmx-users] Re: polymer duplicate atoms I follow your advice to edit the bond conditions of residues Fbg and Fen in my rtp file. Subsequently, I should modify the hdb file to add hydrogens for Fbg and Fen. However, I get the fatal error message Atom +C1 not found in residue Fbg 113, rtp entry Fbg while adding hydrogens. I can successfully generate the structure (conf.gro) when I am using pdb2gmx command(pdb2gmx -ff oplsaa -f 2.pdb -q -missing) with the -missing option and ignoring the hdb file. ; rtp file [ Fbg ] [ bonds ] C5+C1 C5H51 C5H52 C5H53 [ Fen ] [ bonds ] C6-C4 C6H11 C6H12 C6H13 ; hdb file Fbg 1 3 4 H C5 +C1 +C2 Fen 1 3 4 H C6 -C4 -C3 f2311-differ_residue_num.pdb http://gromacs.5086.n6.nabble.com/file/n5006479/f2311- differ_residue_num.pdb -- View this message in context: http://gromacs.5086.n6.nabble.com/polymer-duplicate-atoms- tp5006328p5006479.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
